OPENSEQ.org - 1416337432 - GREMLIN Submission

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ompla

ID:	1416337432	Query Sequence MRTLQGWLLPVFMLPMAVYAQEATVKEVHDAPAVRGSIIANMLQEHDNPFTLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	289 (257)
Sequences:	302 (208)
Seq/Len:	1.175
Nf(neff/√len):	13.0

HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.175).

Sequences per length for each position, AFTER the coverage/gap filter was applied

Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

i	j	Scaled score	Prob
249_Y	257_L	3.319	1.00
131_E	270_I	3.159	1.00
242_G	262_Y	2.948	1.00
231_K	242_G	2.801	1.00
194_K	216_Q	2.669	1.00
159_G	179_Y	2.467	0.99
198_V	203_D	2.440	0.99
88_K	260_Q	2.427	0.99
161_N	179_Y	2.240	0.99
261_V	277_T	2.161	0.98
87_V	120_L	2.143	0.98
55_Y	94_A	2.131	0.98
191_V	217_L	2.021	0.97
263_S	275_N	2.001	0.97
234_Y	239_G	1.917	0.95
116_S	132_T	1.903	0.95
108_L	140_L	1.900	0.95
139_F	159_G	1.782	0.93
160_Y	176_N	1.700	0.90
94_A	121_S	1.675	0.89
128_P	172_S	1.665	0.89
63_T	280_G	1.650	0.88
52_L	285_L	1.631	0.87
135_E	161_N	1.618	0.87
244_E	260_Q	1.551	0.84
226_A	247_L	1.519	0.82
98_W	101_I	1.517	0.82
163_D	255_V	1.511	0.81
114_Q	134_Y	1.501	0.81
133_N	167_R	1.501	0.81
159_G	180_T	1.472	0.79
123_S	210_K	1.429	0.76
159_G	258_Y	1.427	0.76
189_W	221_Y	1.425	0.76
52_L	97_L	1.402	0.74
38_I	42_M	1.398	0.74
106_S	179_Y	1.389	0.73
214_Y	244_E	1.366	0.71
158_M	180_T	1.362	0.71
139_F	179_Y	1.340	0.69
204_D	271_D	1.283	0.64
241_G	262_Y	1.279	0.64
251_I	257_L	1.277	0.64
263_S	277_T	1.271	0.63
111_S	137_Q	1.267	0.63
63_T	278_R	1.249	0.61
150_G	186_N	1.245	0.61
86_E	119_Q	1.240	0.61
89_F	103_G	1.235	0.60
52_L	231_K	1.225	0.59
258_Y	280_G	1.224	0.59
69_N	271_D	1.211	0.58
246_G	260_Q	1.211	0.58
94_A	250_P	1.205	0.57
67_D	108_L	1.196	0.56
135_E	163_D	1.193	0.56
198_V	268_S	1.191	0.56
246_G	284_M	1.190	0.56
61_I	258_Y	1.190	0.56
233_Q	242_G	1.187	0.56
55_Y	151_W	1.179	0.55
65_T	276_Q	1.179	0.55
209_T	251_I	1.177	0.55
96_P	107_V	1.177	0.55
151_W	189_W	1.167	0.54
160_Y	178_L	1.167	0.54
113_T	281_V	1.167	0.54
109_G	170_P	1.160	0.53
161_N	208_I	1.141	0.51
35_R	111_S	1.141	0.51
138_L	160_Y	1.139	0.51
91_L	152_T	1.139	0.51
210_K	238_T	1.135	0.51
105_N	112_Y	1.134	0.50
114_Q	153_L	1.133	0.50
59_Y	94_A	1.129	0.50
172_S	204_D	1.129	0.50
106_S	142_F	1.125	0.50
250_P	257_L	1.123	0.49
50_F	176_N	1.118	0.49
216_Q	275_N	1.113	0.48
50_F	91_L	1.113	0.48
120_L	160_Y	1.109	0.48
86_E	137_Q	1.098	0.47
230_A	243_A	1.093	0.47
232_G	236_W	1.092	0.46
39_I	44_Q	1.091	0.46
112_Y	140_L	1.087	0.46
163_D	175_W	1.085	0.46
246_G	258_Y	1.079	0.45
58_N	204_D	1.074	0.45
61_I	280_G	1.069	0.44
117_W	278_R	1.068	0.44
175_W	198_V	1.065	0.44
119_Q	280_G	1.063	0.44
127_S	249_Y	1.060	0.43
41_N	48_N	1.038	0.41
109_G	183_M	1.038	0.41
216_Q	233_Q	1.038	0.41
86_E	130_R	1.035	0.41
194_K	262_Y	1.030	0.41
212_M	242_G	1.026	0.40
208_I	212_M	1.026	0.40
175_W	196_W	1.026	0.40
119_Q	137_Q	1.022	0.40
138_L	251_I	1.021	0.40
267_E	279_V	1.017	0.39
172_S	267_E	1.016	0.39
134_Y	167_R	1.013	0.39
276_Q	280_G	1.009	0.39
57_T	288_L	1.006	0.38
267_E	280_G	1.005	0.38
128_P	204_D	1.004	0.38
39_I	43_L	1.003	0.38
236_W	239_G	1.003	0.38

Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).

Text file of contact predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

NEW Features

See coupling matrix (for protein design or mutagenesis)
Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.

HHsearch Results: (06Sep14)
GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.

PDB	M	Cov	P(%)	HHΔ
1qd5A	1	0.8893	100	0.095	Contact Map
1qd6C	2	0.8304	100	0.154	Contact Map
2x9kA	1	0.5606	42.5	0.968	Contact Map
4e1sA	1	0.526	18	0.974	Contact Map
2o4vA	3	0.3702	8.4	0.977	Contact Map
4fqeA	1	0.2941	5.4	0.979	Contact Map
1vw4a	1	0.2076	3.3	0.981	Contact Map
3qraA	1	0.3945	2.5	0.982	Contact Map
2r18A	1	0.1626	2.4	0.983	Contact Map
4e1tA	1	0.5571	2.4	0.983	Contact Map

M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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